Japan has been expected to push for a reopening of the investigation into the fate of the abductees, kidnapped in the 1970s and 1980s to train North Korean spies.
The issue, a hugely emotional one in Japan, was already brought up in an earlier bilateral meeting held in China in March.
Japan has reportedly told the North Korean head negotiator, Song Il Ho, that it is willing to lift some economic sanctions if there is evidence that Pyongyang is making a serious effort to investigate the case, according to Kyodo News, which cited unnamed sources.
Five of the abductees were allowed to return to Japan but Pyongyang has insisted, without producing solid evidence, that the eight others are dead.
Other issues thought to be on the agenda are the North Korean hermit state's missile and nuclear weapons programmes, but the delegations have remained tightlipped so far.
"We had intense, serious and frank discussions," Japanese chief delegate Junichi Ihara, director general of the foreign ministry's Asian and Oceanian Affairs Bureau, said at a press conference after the first day of talks.
"As only the first day is over, I'd like to refrain from making comments that could give any prejudgment over the course of the talks," he added.
The three-day meeting will end .